[INFO] Packaging your application as a native app...
[INFO] The application was successfully packaged
The application was successfuly signed
Only iOS simulator is supported to run packaged apps
Failed to run packaged application

I don't get any errors now. The Entitlements Certificate had an error in the prefixed (.) in the App ID string. I get the above now.

[INFO] Packaging your application as a native app...
[INFO] The application was successfully packaged
The application was successfuly signed
Only iOS simulator is supported to run packaged apps
Failed to run packaged application

I don't get any errors now. The Entitlements Certificate had an error in the prefixed (.) in the App ID string. I get the above now.

However the application still doesn't install

Finally I was able to install the application onto my iPad.Below are the sequence of steps that I did to get it working.

I dragged the SampleApp.app into the organizer window in Xcode in Applications. The console window gave the list of errors. I found that this was the error.

The executable was signed with invalid entitlements.

Entitlements was getting screwed up though the application was signed properly.

@vikramiyer's solution worked for me too eventually. Too slow to be practical in my workflow though, I'll probably have to use phonegap for now but will follow Sencha CMD closely 'cause I'm so close to having it work properly (works great in simulator) and I think it might be more convenient than phonegap for simple projects that don't need to integrate with 3rd party obj-c frameworks / xcode projects.

Turns out though xcode can automate the device provisioning and stuff, when I looked in the iphone dev provisioning portal there was in fact a mismatch with the provisioning profile so I created another profile and removed old ones and it's now working for my iPhone 5 just not my iPhone 3Gs for some reason. I'll debug that later, maybe another mismatch I overlooked.

I suspect the reason @vikramiyer' codesigning solution worked is that xcode is possibly a little smarter than sencha cmd at guessing which profile to use or something like that.